Activators for oligonucleotide synthesis

ABSTRACT

A process for the sysnthesis of oligonucleotides using phosphoramidite chemistry is provided. The process employs as activator a 1,1-dioxo-1,2-dihydro-1λ 6 -benzo[d]isothiazol-3-one, preferably in the presence of an organic base. The 1,1-dioxo-1,2-dihydro-1λ 6 -benzo[d]isothiazol-3-one is represented by the following structural formula:  
                 
 
wherein p is 0 or an integer from 1 to 4; X 7  is O or S; R for each occurrence is a substituent, preferably each independently, a halo, a substituted or unsubstituted aliphatic group, —NR 11 R 12 , —OR 13 , —OC(O)R 13 , —C(O)OR 13 , or cyano; or two adjacent R groups taken together with the carbon atoms to which they are attached form a six membered saturated or unsaturated ring; R 11  and R 12  are each, independently, —H, a substituted or unsubstituted aliphatic group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted aralkyl group; and R 13  is a substituted or unsubstituted aliphatic group, a substituted or unsubstituted aryl group, or a substituted or unsubstituted aralkyl group. Preferred organic bases are pyridine, 3-methylpyridine, or N-methylimidazole.

BACKGROUND OF THE INVENTION

Synthetic oligonucleotides are important diagnostic tools for thedetection of genetic and viral diseases. In addition, oligonucleotidesand modified oligonucleotides are of interest as therapeutic candidatesthat inhibit gene expression or protein function. Large scale synthesisof oligonucleotides for use as therapeutic candidates has becomeincreasingly important since FDA approval of an oligonucleotide analogfor the treatment of cytomegalovirus (CMV), and several otheroligonucleotide analogs are currently in clinical trials. Kilogramquantities of a purified oligonucleotide analog are needed for eachclinical trial.

Preparation of an oligonucleotide using phosphoramidite methodologyinvolves condensation of a nucleoside phosphoramidite and a nucleosideor a nascent oligonucleotide. The condensation reaction (also referredto herein as the coupling reaction) requires an activator (alternativelyknown as a coupling agent) which facilitates the reaction. The mostcommonly used activator is the nucleophilic activator 1H-tetrazole.However, 1H-tetrazole is explosive and, therefore, can be hazardous touse in large scale syntheses.

1H-tetrazole is a weak acid which protonates the trivalent phosphorus ofthe phosphoramidite during the first step of activation. A tetrazolideanion then displaces the dialkylamine group (e.g., N,N-diisopropylamine) of the phosphoramidite during a second slower step to form atetrazolyl intermediate which then reacts rapidly with the 5′-primaryalcohol group of a nucleoside or a nascent oligonucleotide. Whensterically hindered phosphoramidites, such as t-butyl-dimethylsilylprotected ribonucleoside phosphoramidites or 2′-O-methylnucleosidephosphoramidites, are used for oligonucleotide synthesis alternativeactivators are often needed to increase the rate of the couplingreaction. Alternative activators, such as 5-ethylthio-1H-tetrazole,5-(p-nitrophenyl)-1H-tetrazole, and benzimidazolium triflate, are oftenmore acidic than tetrazole and, thus, accelerate the rate of protonationof the trivalent phosphorous thereby increasing the rate ofcondensation.

However, since tetrazole, 5-ethylthio-1H-tetrazole,5-(p-nitrophenyl)-1H-tetrazole, and benzimidazolium triflate are acidic,they can cause premature deprotection of the 5′-hydroxy protecting groupof a phosphoramidite monomer which is typically an acid labile group.Premature deprotection can produce oligonucleotide impurities that areone base longer than the desired product (referred to herein as “N+1impurities”) and are difficult to separate from the desired product. Thelonger coupling times generally necessary for RNA synthesis and largescale synthesis result in an increase in premature deprotection ofphosphoramidites.

Therefore, non-explosive activators that promote condensation of anucleoside phosphoramidite with a nucleoside or a nascentoligonucleotide and which may be employed without increasing sideproducts are needed in order to make oligonucleotides more readilyavailable for diagnostic and therapeutic use.

SUMMARY OF THE INVENTION

It has been discovered that a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one will promotecondensation of a nucleoside phosphoramidite and nucleoside monomer or anascent oligonucleotide. The1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one can be represented byStructural Formula I:

In Structural Formula I, p is 0 or an integer from 1 to 4. R for eachoccurrence is a substituent, preferably each independently, a halo, asubstituted or unsubstituted aliphatic group, —NR¹¹R¹², —OR¹³,—OC(O)R¹³, —C(O)OR¹³, cyano, a substituted or unsubstituted aryl, asubstituted or unsubstituted heterocyclyl, —CHO, —COR¹³, —NHCOR¹³, asubstituted or unsubstituted aralkyl, halogenated alkyl (e.g.,trifluoromethyl and trichloromethyl), or —SR¹³. Preferably, R is halo, asubstituted or unsubstituted aliphatic group, —NR¹¹R¹², —OR¹³,—OC(O)R¹³, —C(O)OR¹³, or cyano. Alternatively, two adjacent R groupstaken together with the carbon atoms to which they are attached form asix membered saturated or unsaturated ring. Preferably, the six memberedring formed is an aromatic ring. R¹¹ and R¹² are each, independently,—H, a substituted or unsubstituted aliphatic group, a substituted orunsubstituted aryl group, a substituted or unsubstituted aralkyl group;or together with the nitrogen to which they are attached form aheterocyclyl group. R¹³ is a substituted or unsubstituted aliphaticgroup, a substituted or unsubstituted aryl group, or a substituted orunsubstituted aralkyl group. X⁷ is O or S. Preferably, X⁷ is O. It isparticularly preferred that X⁷ is O and p is 0.

In a preferred embodiment, a salt complex of the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and an organic basecan be used to efficiently promote condensation of a nucleosidephosphoramidite and nucleoside monomer or a nascent oligonucleotide.Thus, one embodiment of the invention is a salt complex of the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one represented byStructural Formula I and an organic base.

In the presence of an organic base,1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one has good solubilityparticularly in organic solvents that are typically used foroligonucleotide synthesis. Therefore, another embodiment of theinvention is an activator solution that includes an organic solvent, anorganic base and a 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-onerepresented by Structural Formula I. The concentration of the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and the organic basein the activator solution can be up to the solubility of the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one in the solventconcerned. In a preferred embodiment, the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and the organic baseare present in a concentration range of about 0.01 M to about 2M, forexample from about 0.05M to about 0.5M. Commonly, the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and the organic baseare present at a concentration of up to 0.25M, such as from about 0.1 Mto about 0.25M. In a more preferred embodiment, the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and the organic baseare present in the same molar concentration. In a preferred embodiment,the organic solvent comprises acetonitrile. In another preferredembodiment, the organic solvent comprises an organic amide, such asdimethylformamide, 1-methyl-2-pyrrolidinone or1,3-dimethyl-2-imidazolidinone.

In another embodiment, an oligonucleotide can be synthesized usingphosphoramidite chemistry in which the coupling agent is a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one represented byStructural Formula I. The coupling agent promotes condensation between anucleoside or a nascent oligonucleotide having a free hydroxy or thiolgroup and a phosphoramidite. In a preferred embodiment, an organic baseis present with the 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-oneduring the coupling reaction. In a more preferred embodiment, theorganic base is present in the same molar concentration as the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one.

The nucleoside phosphoramidite can be a monomer or an oligomer, such asa dimer or a trimer. When the nucleoside phosphoramidite is a monomer itcan be represented by represented by Structural Formula IIa:

In Structural Formula IIa, X¹ for each occurrence is, independently, —O—or —S—. Preferably, X¹ is —O— at every occurrence. X² for eachoccurrence is, independently, —O—, —S—, or —NR—. Preferably, X² is —O—at every occurrence. X³ for each occurrence is, independently, —O—, —S—,—CH₂—, or —(CH₂)₂—. Preferably, X³ is —O— at every occurrence. In a morepreferred embodiment, X¹, X², and X³ are all —O— at every occurrence. R¹is an alcohol protecting group or a thio protecting group. Preferably,R¹ is an acid labile protecting group. R² for each occurrence is,independently, —H, —F —OR⁶, —NR⁷R⁸, —SR⁹, or a substituted orunsubstituted aliphatic group, such as methyl or allyl. R³ for eachoccurrence is, independently, —OCH₂CH₂CN, —SCH₂CH₂CN, a substituted orunsubstituted aliphatic group, —OR¹⁰, —SR¹⁰, —O—CH₂CH₂—Si(CH₃)₂C₆H₅,—O—CH₂CH₂—S(O)₂—CH₂CH₃, —O—CH₂CH₂—C₆H₄—NO₂, —S—CH₂CH₂—Si(CH₃)₂C₆H₅,—S—CH₂CH₂—S(O)₂—CH₂CH₃, or —S—CH₂CH₂—C₆H₄—NO₂. R⁴ and R⁵ are each,independently, a substituted or unsubstituted aliphatic group, asubstituted or unsubstituted aryl group, a substituted or unsubstitutedaralkyl. Alternatively, R⁴ and R⁵ taken together with the nitrogen towhich they are bound form a heterocyclyl group. R⁶ for each occurrenceis, independently, —H, a substituted or unsubstituted aliphatic group(e.g., methyl, ethyl, methoxyethyl or allyl), a substituted orunsubstituted aryl group, a substituted or unsubstituted aralkyl, analcohol protecting group, or —(CH₂)_(q)—NR¹⁸R¹⁹. R⁷ and R⁸ for eachoccurrence are each, independently, —H, a substituted or unsubstitutedaliphatic group, or an amine protecting group. Alternatively, R⁷ and R⁸taken together with the nitrogen to which they are attached are aheterocyclyl group. R⁹ for each occurrence is, independently, —H, asubstituted or unsubstituted aliphatic group, or a thio protectinggroup. R¹⁰ is for each occurrence is, independently, a substituted orunsubstituted aliphatic group, a substituted or unsubstituted aryl groupor a substituted or unsubstituted aralkyl group. R¹⁸ and R¹⁹ are each,independently, —H, a substituted or unsubstituted aryl group, asubstituted or unsubstituted heteroaryl group, a substituted orunsubstituted aliphatic group, a substituted or unsubstituted aralkylgroup, a substituted or unsubstituted heteroaralkyl group or an amineprotecting group. Alternatively, R¹⁸ and R¹⁹ taken together with thenitrogen to which they are attached form a heterocyclyl group. q is aninteger from 1 to about 6. B is —H, a natural or unnatural nucleobase,protected nucleobase, protected natural or unnatural nucleobase,heterocycle or a protected heterocycle.

In another embodiment, the phosphoramidite can be an oligomer, such as adimer or trimer. Methods of preparing and utilizing nucleosidephosphoramidite dimers and trimers in phosphoramidite synthesis ofoligonucleotides are disclosed in International Patent Application No.PCT/GB01/03973, the entire teachings of which are incorporated herein byreference.

The sugar moiety of the nucleoside phosphoramidite can have either a Dconfiguration, as in naturally occurring DNA and RNA and as inStructural Formula IIa, or it can have an L configuration. StructuralFormula lib represents an L-nucleoside phosphoramidite:

In Structural Formula IIb, X¹, X², X³, R¹, R², R³, R⁴, R⁵, and B are asdefined above.

In another embodiment, the phosphoramidite group of the nucleosidephosphoramidite can be attached to the 5′-position of the sugar ring. Inthis embodiment, the nucleoside phosphoramidite can be represented byStructural Formulae IIIa and IIIb:

In Structural Formulas IIIa and IIIb, X¹, X², X³, R¹, R², R³, R⁴, R⁵,and B are as defined above.

In another embodiment, the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one can be used topromote condensation of a nascent n-mer oligonucleotide (i.e., anoligonucleotide having n nucleobases) and a nucleoside phosphoramiditeto form an (n+1)-mer oligonucleotide. Preferably, the nucleosidephosphoramidite can be represented by Structural Formula IIa. Thenascent oligonucleotide can be represented by Structural Formula IV:

In Structural Formula IV, X¹, X², X³, R², R³, and B are as definedabove. Each X⁴ for each occurrence is, independently, O or S. X⁵ foreach occurrence is, independently, —OH or —SH. Preferably, X⁵ is —OH.R¹⁶ is a hydroxy protecting group, a thio protecting group, an aminoprotecting group, —(CH₂)_(q)—NR¹⁸R¹⁹, a solid support, or a cleavablelinker attached to a solid support, such as a group of the formula—Y²-L-Y²—R¹⁵. Y² for each occurrence is, independently, a single bond,—C(O)—, —C(O)NR¹⁷—, —C(O)O—, —NR¹⁷— or —O—. L is a linker which ispreferably a substituted or unsubstituted aliphatic group or asubstituted or unsubstituted aromatic group. More preferably, L is anethylene group. R¹⁷ is —H, a substituted or unsubstituted aliphaticgroup or a substituted or unsubstituted aromatic group. R¹⁵ is any solidsupport suitable for solid phase oligonucleotide synthesis known tothose skilled in the art. Examples of suitable solid supports includecontrolled-pore glass, polystyrene, microporous polyamide, such aspoly(dimethylacrylamide), and polystyrene coated with polyethylene. Inmany embodiments, R¹⁶ represents a cleavable linker, such as a succinylor oxaloyl linker, attached to a solid support. n is zero or a positiveinteger.

The nascent oligonucleotide is contacted with the phosphoramidite and a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one represented byStructural Formula I. In a preferred embodiment, an organic base is alsopresent when the nascent oligonucleotide is contacted with the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one. More preferably, theorganic base is present in the same molar concentration as the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one. The nascentoligonucleotide reacts with the phosphoramidite to form an (n+1)oligonucleotide having a 5′-terminal trivalent phosphorous linkagerepresented by Structural Formula V:

In Structural Formula V, X¹, X², X³, X⁴, R¹, R², R³, R¹⁶, B and n aredefined as above.

The oligonucleotide represented by Structural Formula V can then becontacted with an oxidizing agent or a sulfurizing agent to form anoligonucleotide having a pentavalent phosphorous backbone represented byStructural Formula VI:

In Structural Formula VI, X¹, X², X³, X⁴, R¹, R², R³, R¹⁶, B and n aredefined as above.

After oxidizing or sulfurizing the (n+1) oligonucleotide, X⁵ groupswhich did not react with the phosphoramidite can be capped byconventional capping techniques known in the art. For example, theunreacted X⁵ groups can be reacted with an acid chloride or an anhydridein the presence of a base. Typically, X⁵ groups are capped with acetylchloride or acetic anhydride in pyridine.

After the oxidation or sulfurization step or after the capping step, the(n+1) oligonucleotide can be deprotected by reacting it with a reagentto remove R¹. If R¹ is an acid labile protecting group, the (n+1)oligonucleotide is treated with an acid to remove R¹. If R¹ is atrialkylsilyl group, such as t-butyldimethylsilyl group or atriisopropylsilyl group, the (n+1) oligonucleotide can be treated withfluoride ions to remove R¹. Typically, t-butyldimethylsilyl and atriisopropylsilyl are removed by treatment with a solution oftetrabutylammonium fluoride in THF or with hydrogen fluoride and aconjugate base, such as (C₂H₅)₃N.3HF. Methods for removingt-butyldimethylsilyl can be found in Greene, et al., Protective Groupsin Organic Synthesis (1991), John Wiley & Sons, Inc., pages 77-83, theteachings of which are incorporated herein by reference in theirentirety. The above reaction steps, or reaction cycle, can be repeatedone or more times to form an oligonucleotide of the desired length. Whenit is desired to obtain an oligonucleotide product in which the 5′-endgroup is protected, the final step of the reaction cycle can be thecapping step, if a capping step is done, or the final step of thereaction can be an oxidation or sulfurization step if a capping step isnot done. When the oxidation or sulfurization step or the capping stepis the final step, the oligonucleotide can be represented by StructuralFormula VII:

In Structural Formula VII, X¹, X², X³, X⁴, R¹, R², R³, R¹⁶, and B aredefined as above. m is an integer.

Alternatively, the final step of the reaction cycle can be removal of R¹if it is desired to obtain an oligonucleotide which does not have a5′-protecting group. When removal of R¹ is the final reaction step, theoligonucleotide can be represented by Structural Formula VIII:

In Structural Formula VIII, X¹, X², X³, X⁴, X⁵, R¹, R², R³, R¹⁶, B and mare defined as above.

Oligonucleotides produced by the method of the present invention can bedeprotected, and as appropriate cleaved from a solid support, usingmethods known in the art for the given protecting groups and/or solidsupport.

1,1-Dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-ones in the presence ofan organic base promote phosphoramidite condensation reactions with atleast equal efficiency as tetrazole. However, fewer undesirable sideproducts are produced when a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one is used instead oftetrazole. In addition, the complexes of the invention are non-explosiveand therefore, safer to use than tetrazole particularly in large scalesynthesis of oligonucleotides.

DETAILED DESCRIPTION OF THE INVENTION

Aliphatic groups, as used herein, include straight chained or branchedC₁-C₁₈ hydrocarbons which are completely saturated or which contain oneor more unconjugated double bonds, or cyclic C₃-C₁₈ hydrocarbons whichare completely saturated or which contain one or more unconjugateddouble bonds. Alkyl groups are straight chained or branched C₁-C₈hydrocarbons or C₃-C₈ cyclic hydrocarbons which are completelysaturated. Aliphatic groups are preferably alkyl groups.

Aryl groups include carbocyclic aromatic ring systems (e.g., phenyl) andcarbocyclic aromatic ring systems fused to one or more carbocyclicaromatic (e.g., naphthyl and anthracenyl) or an aromatic ring systemfused to one or more non-aromatic ring (e.g.,1,2,3,4-tetrahydronaphthyl).

Heterocyclic groups, as used herein, include heteroaryl groups andheteroalicyclyl groups. Heteroaryl groups, as used herein, includearomatic ring systems that have one or more heteroatoms selected fromsulfur, nitrogen or oxygen in the aromatic ring. Preferably, heteroarylgroups are five or six membered ring systems having from one to fourheteroatoms. A heteroalicyclyl group, as used herein, is a non-aromaticring system that preferably has five to six atoms and includes at leastone heteroatom selected from nitrogen, oxygen, and sulfur. Examples ofheterocyclic groups include morpholinyl, piperidinyl, piperazinyl,thiomorpholinyl, pyrrolidinyl, thiazolidinyl, tetrahydrothienyl,azetidinyl, tetrahydrofuryl, dioxanyl and dioxepanyl thienyl, pyridyl,thiadiazolyl, oxadiazolyl, indazolyl, furans, pyrroles, imidazoles,pyrazoles, triazoles, pyrimidines, pyrazines, thiazoles, isoxazoles,isothiazoles, tetrazoles, oxadiazoles, benzo(b)thienyl, benzimidazole,indole, tetrahydroindole, azaindole, indazole, quinoline,imidazopyridine, purine, pyrrolo[2,3-d]pyrimidine, andpyrazolo[3,4-d]pyrimidine.

Azaheterocyclyl compounds, as used herein, include heteroaryl groupswhich have one or more nitrogen atom in the aromatic ring andheteroalicyclyl groups that have at least one nitrogen atom in thenon-aromatic ring system. Preferably, azaheteroaryl compounds have five-or six-membered aromatic rings with from one to three nitrogens in thearomatic ring. Preferably, azaheteroalicyclyl compounds are five- orsix-membered rings, commonly comprising one or two nitrogens in thering. Preferred azaheterocyclyl compounds are organic bases. Examples ofazaheterocyclyl compounds that are organic bases include pyrimidines,1-alkylpyrazoles, especially 1-(C₁₋₄ alkyl)pyrazoles, 1-arylpyrazoles,1-benzylpyrazoles, pyrazines, N-alkylpurines, especially N—(C₁₋₄alkyl)purines, N-arylpurines, N-benzylpurines, N-alkylpyrroles,especially N—(C₁₋₄ alkyl)pyrroles, N-arylpyrroles, N-benzylpyrroles,pyridines, N-alkylimidazoles, especially N—(C₁₋₄ alkyl)imidazoles,N-arylimidazoles, especially N-phenylimidazole, N-benzylimidazoles,quinolines, isoquinolines, quinoxalines, quinazolines, N-alkylindoles,especially N—(C₁₋₄ alkyl)indoles, N-arylindoles, N-benzylindoles,N-alkylbenzimidazoles especially N—(C₁₋₄ alkyl)benzimidazoles,N-arylbenzimidazoles, N-benzylbenzimidazoles, triazine, thiazole,1-alkyl-7-azaindoles, especially 1-(C₁₋₄ alkyl)-7-azaindoles,1-aryl-7-azaindoles, 1-benzyl-7-azaindoles, pyrrolidines, morpholines,piperidines, and piperazines. Especially preferred azaheterocyclylcompounds are pyridines, such as pyridine and 3-methylpyridine, andN—(C₁₋₄ alkyl) imidazoles, such as N-methylimidazole.

An aralkyl group, as used herein, is an aromatic substituent that islinked to a moiety by an alkyl group. Preferred aralkyl groups includebenzyl groups.

A heteroaralkyl group, as used herein, is a heteroaryl substituent thatis linked to a moiety by an alkyl group.

An organic base is an organic compound that has a tendency to acceptprotons at pH 7. Preferred organic bases are secondary amines, tertiaryamines or azaheterocyclyl compounds, each of which may be substituted orunsubstituted by one or more substituents. An aprotic organic base is anorganic base that has no hydrogen bonding protons in its chemicalstructure before accepting a proton. Aprotic organic bases such astertiary amines and aprotic azaheterocyclyl compounds are preferablyused in conjunction with1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-ones, as describedherein, to promote condensation reactions.

Tertiary amines are organic bases that have a nitrogen atom which isbonded to three carbon atoms, often to three aryl, commonly phenyl,and/or alkyl groups, commonly to three alkyl groups, including forexample trialkylamines such as trimethylamine, triethylamine, anddiisopropylethylamine. In addition, tertiary amines can beazaheterocyclyl groups wherein the nitrogen atom is aprotic. Tertiaryamines that are azaheterocyclyl groups are preferred. Examples ofazaheterocyclyl tertiary amines are N-alkylpyrrolidines,N-arylpyrrolidines, N-alkylpyrroles, N-arylpyrroles, N-alkylmorpholines,N-arylmorpholines, N-alkylpiperidines, N-arylpiperidines,N,N-dialkylpiperazines, N,N-diarylpiperazines,N-alkyl-N-aryl-piperazines, quinuclidines, and1,8-diazabicyclo[5.4.0]undec-7-enes. Tertiary amines can also beazaheteroaryl or azaheteroalicyclyl compounds.

Secondary amines are organic bases comprising a nitrogen bonded to asingle hydrogen and to two carbon atoms. Commonly the nitrogen atom isbonded to two alkyl or aryl groups or forms part of an azaheterocyclicgroup. Examples of secondary amine compounds include diethylamine anddiisopropylamine.

Suitable substituents for aliphatic groups, aryl groups, aralkyl groups,heteroaryl groups, azaheteroaryl groups and heteroalicyclyl groupsinclude aryl groups, halogenated aryl groups, alkyl groups, halogenatedalkyl (e.g. trifluoromethyl and trichloromethyl), aliphatic ethers,aromatic ethers, benzyl, substituted benzyl, halogens, particularlychloro and fluoro groups, cyano, nitro, —S-(aliphatic or substitutedaliphatic group), and —S— (aromatic or substituted aromatic).

Amine, hydroxy and thiol protecting groups are known to those skilled inthe art. For examples of amine protecting groups see Greene, et al.,Protective Groups in Organic Synthesis (1991), John Wiley & Sons, Inc.,pages 309-405, the teachings of which are incorporated herein byreference in their entirety. Preferably, amines are protected as amidesor carbamates. For examples of hydroxy protecting groups see Id., pages10-142, the teachings of which are incorporated herein by reference intheir entirety. A preferred hydroxy protecting group ist-butyldimethylsilyl group. For examples of thiol protecting groups seeId., pages 277-308, the teachings of which are incorporated herein byreference in their entirety.

An acid labile protecting group is a protecting group which can beremoved by contacting the group with a Bronsted or a Lewis acid. Acidlabile protecting groups are known to those skilled in the art. Examplesof common acid labile protecting groups include substituted orunsubstituted trityl groups (Id., pages 60-62), substituted orunsubstituted tetrahydropyranyl groups (Id., pages 31-34), substitutedor unsubstituted tetrahydrofuranyl groups (Id., pages 36-37) or pixylgroups (Id., page 65). Trityl groups are commonly substituted byelectron donating substituents such as alkoxy groups. A preferred acidlabile protecting group is a substituted or unsubstituted trityl, forexample 4,4′-dimethoxytrityl (hereinafter “DMT”).

Nucleoside bases include naturally occurring bases, such as adenine,guanine, cytosine, thymine, and uricil and modified bases such as7-deazaguanine, 7-deaza-8-azaguanine, 5-propynylcytosine,5-propynyluricil, 7-deazaadenine, 7-deaza-8-azaadenine,7-deaza-6-oxopurine, 6-oxopurine, 3-deazaadenosine,2-oxo-5-methylpyrimidine, 2-oxo-4-methylthio-5-methylpyrimidine,2-thiocarbonyl-4-oxo-5-methylpyrimidine, 4-oxo-5-methylpyrimidine,2-amino-purine, 5-fluorouricil, 2,6-diaminopurine, 8-aminopurine,4-triazolo-5-methylthymine, and 4-triazolo-5-methyluricil.

A protected nucleoside base is a nucleoside base in which reactivefunctional groups of the base are protected. Similarly, a protectedheterocycle is a heterocycle in which reactive substitutents of theheterocycle are protected. Typically, nucleoside bases or heterocycleshave amine groups which can be protected with an amine protecting group,such as an amide or a carbamate. For example, the amine groups ofadenine and cytosine are typically protected with benzoyl protectinggroups, and the amine groups of guanine is typically protected with anisobutyryl group, an acetyl group or t-butylphenoxyacetyl group.However, other protection schemes may be used. For example, for fastdeprotection, the amine groups of adenine and guanine are protected withphenoxyacetyl groups and the amine group of cytosine is protected withan isobutyryl group or an acetyl group. Conditions for removal of thenucleobase or heterocycle protecting group will depend on the protectinggroup used. When an amide protecting group is used, it can be removed bytreating the oligonucleotide with a base solution, such as aconcentrated ammonium hydroxide solution, n-methylamine solution or asolution of t-butylamine in ammonium hydroxide.

The term “oligonucleotide,” as used herein, includes naturally occurringoligonucleotides, for example 2′-deoxyribonucleic acids (hereinafter“DNA”) and ribonucleic acids (hereinafter “RNA”) and nucleic acidscontaining modified sugar moieties, modified phosphate moieties, ormodified nucleobases. Modification to the sugar moiety includesreplacing the ribose ring with a hexose, cyclopentyl or cyclohexyl ring.Alternatively, the D-ribose ring of a naturally occurring nucleic acidcan be replaced with an L-ribose ring or the b-anomer of a naturallyoccurring nucleic acid can be replaced with the a-anomer. Theoligonucleotide may also comprise one or more abasic moieties. Modifiedphosphate moieties include phosphorothioates, phosphorodithioates,methyl phosphonates, methyl phosphates, and phosphoramidates. Suchnucleic acid analogs are known to those of skill in the art.Oligonuceotides comprising mixtures of two or more of the foregoing maybe prepared, for example, oligonuceotides comprising mixtures ofdeoxyribo- and ribonucleosides, particularly mixtures ofdeoxyribonucleosides and 2′-O-substituted ribonucelosides, such as2′-O-methyl or 2′-O-methoxyethyl ribonucleosides. Examples ofoligonucleotides comprising mixtures of nucleosides include ribozymes.

A chimeric oligonucleotide is an oligonucleotide that has bothphosphodiester and phosphorothioate linkages.

A synthetic oligonucleotide preferably has from 2 to about 100nucleobases. More preferably, a synthetic oligonucleotide has 2 to about75 nucleobases. Many synthetic oligonucleotides of current therapeuticinterest comprise from 8 to 40 nucleobases.

The synthesis of the oligonucleotide can be done in solution or on asolid support. When the synthesis is in solution, R¹⁶ is an alcohol,amine or thiol protecting group. After synthesis of the oligonucleotidethe alcohol, amine or thiol protecting group can be removed. When theoligonucleotide is synthesized on a solid support, R¹ represents a solidsupport or preferably a cleavable linker attached to a solid support,such as a group of formula —Y₂-L-Y₂—R¹⁵. In general, the solution phasesynthesis or the solid phase synthesis of oligonucleotides using a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one compound instead oftetrazole to promote condensation of a nascent oligonucleotide and aphosphoramidite monomer is carried out similar to method which have beendeveloped for synthesis of oligonucleotides using tetrazole as anactivator. Examples of typical conditions for solution phase synthesisand solid phase synthesis oligonucleotides using a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one compound to promotethe condensation reaction are set forth below.

The first step of preparing the oligonucleotide involves coupling anucleoside phosphoramidite, such as the phosphoramidite represented byStructural Formula IIa, with a nucleoside or nascent oligonucleotidethat has a free hydroxy or thiol group, such as a 5-deprotectednucleoside or nascent oligonucleotide represented by Structural FormulaIV. During the coupling reaction, the hydroxy or thiol group of thenucleoside or nascent oligonucleotide reacts with the nucleosidephosphoramidite by displacing the —NR⁴R⁵ group. When the synthesis isdone in solution, the nucleoside or nascent oligonucleotide is oftenpresent in a concentration of about 0.001 M to about 1.0 M, andpreferably the nucleoside or nascent oligonucleotide is present in aconcentration of about 0.025 M to about 0.5 M. The nucleosidephosphoramidite is preferably present in a concentration of about 1.1equivalents to about 2 equivalents with respect to the nucleoside ornascent oligonucleotide. From about 0.5 equivalents, often from about2.5 equivalents, to about 5.0 equivalents, with respect to thenucleoside or nascent oligonucleotide, of a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one is added to promotethe condensation reaction. Preferably, the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one is added as a saltcomplex with an organic base, such as a pyridinium salt, a 3-picoliniumsalt or an N-methylimidazolium salt. The reaction time is commonly about20 min. to about 60 min., and an (n+1) nascent oligonucleotide with aterminal trivalent phosphorous linkage is formed, such as the nascentoligonucleotide represented by Structural Formula V.

A second step of preparing an oligonucleotide involves oxidizing orsulfurizing the terminal trivalent phosphorous group of the nascentoligonucleotide. In a solution phase synthesis, the oxidation reactionis often carried out by treating the oligonucleotide with an oxidizingagent such as I₂ in the presence of water or a peroxide such as t-butylhydrogen peroxide in an organic solvent. When I₂ and water are used, theoxidizing solution typically contains about 1.1 to about 1.8 equivalentsof I₂ in the presence of a base and a trace amount of water. Thereaction is carried out in an aprotic polar solvent, such as THF,combined with a base, such as a tertiary alkylamine and about 1% water.The ratio of aprotic solvent to base is about 4:1 (vol./vol.) to about1:4 (vol./vol.). After about 5 min. to about 20 min., the reactionmixture is poured into an aqueous solution of sodium bisulfite to quenchthe excess iodine, then extracted into an organic solvent.

Alternatively, the terminal trivalent phosphorous group can besulfurized using any sulfur transfer reagent known to those skilled inthe art of oligonucleotide synthesis. Examples of sulfur transferreagents include 3H-benzodithiol-3-one 1,1-dioxide (also called“Beaucage reagent”), dibenzoyl tetrasulfide, phenylacetyl disulfide,N,N,N′,N′-tetraethylthiuram disulfide, elemental sulfur, and3-amino-[1,2,4]dithiazole-5-thione (see U.S. Pat. No. 6,096,881, theentire teachings of which are incorporated herein by reference).Reaction conditions for sulfurization of an oligonucleotide using theabove reagents can be found in Beaucage, et al., Tetrahedron (1993),49:6123, the teachings of which are incorporated herein by reference intheir entirety. 3-Amino-[1,2,4]dithiazole-5-thione is a preferred sulfurtransfer reagent. Generally, an oligonucleotide is contacted with asolution of 3-amino-[1,2,4]dithiazole-5-thione in an organic solvent,such pyridine/acetonitrile (1:9) mixture or pyridine, having aconcentration of about 0.05 M to about 0.2 M. The sulfurization reactionis commonly complete in about 30 sec. to about 2 min.

After oxidation or sulfurization of the oligonucleotide, any unreactedfree hydroxy or thiol groups can be capped so that they cannot react insubsequent coupling steps. Capping failure sequences allows them to bemore readily separated from full length oligonucleotide product. Anyreagent which will react with a hydroxy or thiol group and prevent itfrom reacting with a phosphoramidite can be used as a capping reagent.Typically, an anhydride, such as acetic anhydride or isobutyricanhydride, or an acid chloride, such as acetyl chloride or isobutyrylchloride, in the presence of a base is used as a capping reagent.

After the capping reaction is complete, the R¹ protecting group isremoved. When R¹ is an acid labile protecting group, R¹ is removed bytreating the oligonucleotide with an acid. Preferably, R¹ is a tritylgroup, such as 4,4′-dimethoxytrityl. When the R¹ is a trityl group, itcan be removed by treating the oligonucleotide with a solution ofdichloroacetic acid or trichloroacetic acid in an organic solvent, suchas dichloromethane or toluene. Once the R¹ protecting group has beenremoved, the reaction cycle (i.e., coupling step, oxidation orsulfurization step, capping step (optional) and deprotection step)optionally can be repeated one or more times to obtain anoligonucleotide of the desired length.

A chimeric oligonucleotide can be prepared by oxidizing the terminaltrivalent phosphorous group in one or more reaction cycles andsulfurizing the terminal trivalent phosphorous group in one or moredifferent reaction cycles. Alternatively, a chimeric oligonucleotide canbe prepared by selecting phosphoramidite monomers in which some of theR³ groups are protected hydroxyl groups, such as —OCH₂CH₂CN, and some ofthe R³ groups are protected thiol groups, such as —SCH₂CH₂CN. In thismethod, the oligonucleotide is oxidized after the coupling step in eachreaction cycle.

When it is desired to obtain an oligonucleotide product in which the R¹group remains, the final step of the reaction cycle can be the cappingstep, if a capping step is done, or the final step of the reaction canbe an oxidation or sulfurization step if a capping step is not done. Ifan R¹ deprotected oligonucleotide is desired, the reaction cycle can endwith the deprotection step. Usually, an R¹ protected oligonucleotide isthe desired product if the oligonucleotide is to be purified by reversephase high performance liquid chromatography (HPLC). If theoligonucleotide is to be purified by ion-exchange chromatography orelectophoresis, an R¹ deprotected oligonucleotide is usually the desiredproduct.

The solid phase synthesis of an oligonucleotide using a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and, preferably, anorganic base to promote condensation of a nucleoside phosphoramiditewith a support bound nucleoside or nascent oligonucleotide having a freehydroxy group of thiol group generally utilizes the same reaction cycleand reagents as the solution phase synthesis. Commonly, the nucleosideis first loaded on the solid support to the maximum suitable for theparticular resin used. For example, loading can be about 50 μmole toabout 700 μmole per gram of support. In the condensation step, asolution of nucleoside phosphoramidite, typically having a concentrationof about 0.01 M to about 1 M, preferably about 0.1 M, in an organicsolvent, such as acetonitrile, is reacted with the support boundnucleoside to form a nascent oligonucleotide having a terminal trivalentphosphorous linkage. If a nucleoside phosphoramidite represented byeither Structural Formula IIa or IIb is used, the nascentoligonucleotide will have a 5′-terminal trivalent phosphorous linkageafter completion of the coupling reaction. If a nucleosidephosphoramidite represented by either Structural Formula IIIa or IIIb isused, the nascent oligonucleotide will have a 3′-terminal trivalentphosphorous linkage after completion of the coupling reaction.Preferably, the nucleoside phosphoramidites used can be represented byStructural Formula IIa. A solution of the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one having aconcentration of about 0.015M to about 1.5 M, often from about 0.05M toabout 0.5M, preferably from 0.1 to 0.25M, is usually mixed with thesolution containing the phosphoramidite monomer just prior to or duringthe condensation reaction. Preferably, an organic base is also presentin the solution at a concentration of about 0.015M to about 1.5 M, oftenfrom about 0.05M to about 0.5M, preferably from 0.1 to 0.25M.Preferably, the organic base is present in the same molar concentrationas the 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one. The1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one may be employed at amole ratio to nucleoside phosphoramidite which is catalytic, that issub-stoichiometric, or at a mole ratio which is stoichiometric orgreater than stoichiometric. In many embodiments, the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to nucleosidephosphoramidite is in the range of for example about 1:1. Then thesupport bound 5′-deprotected nucleoside is contacted with the mixturefor about 2 min. to about 10 min., preferably about 5 min.

If the terminal trivalent phosphorous linkage is to be oxidized afterthe coupling reaction is complete, the solid support containing thenascent oligonucleotide is contacted with an oxidizing agent such as amixture of I₂ and water or a per oxide such as t-butyl hydroperoxide inan organic solvent such as acetonitrile or toluene. A mixture of I₂ andH₂O is a preferred oxidizing reagent. When a mixture of I₂ and water isused other water miscible organic solvents can also be present.Typically, the solid support bound oligonucleotide containing trivalentphosphorous internucleotide linkages can be contacted with a solution OfI₂ in a solvent mixture of water, an aprotic, water miscible solvent,and a base. An example of a typical oxidation solution is about 0.05 Mto about 1.5 M I₂ in a solution of (2:80:20)water/tetrahydrofuran/lutidine (vol./vol./vol.). The solid support istypically treated with the I₂ solution for about 30 seconds to about 1.5min.

Alternatively, the solid support bound nascent oligonucleotide can becontacted with a solution of a sulfur transfer reagent in an organicsolvent to sulfurize the trivalent phosphorous groups. For example, thesupport bound oligonucleotide can be contacted with a solution of3-amino-[1,2,4]-dithiazole-5-thione (about 0.05 M-0.2 M) in an organicsolvent, such as acetonitrile or pyridine, for about 30 sec. to about 2min.

In solid phase oligonucleotide synthesis, the solid support boundnascent oligonucleotide optionally can be contacted with a solution ofthe capping reagent for about 30 sec. to about 1 min. Following thecapping step, the deprotection step is accomplished by contacting thesupport bound oligonucleotide with an acid solution for about 1 min. toabout 3 min. The reaction cycle can optionally be repeated one or moretimes until an oligonucleotide of the desired length is synthesized. Asin the solution phase synthesis, an R¹ protected oligonucleotide isobtained when the reaction cycle ends with either the capping step orthe oxidation or sulfurization step. An R¹ deprotected oligonucleotideis obtained when the reaction cycle is ended with the deprotection step.

When the solid phase synthesis is completed, the oligonucleotide can beremoved from the solid support by standard methods. Generally, the solidsupport is treated with a solution of concentrated ammonium hydroxide at25° C.-60° C. for about 0.5 hours to about 16 hours or longer dependingon the oligonucleotide sequence and whether it is desired to remove thenucleobase protecting groups during this step. The oligonucleotides areadvantageously purified by methods known in the art, such as one or moreof ion-exchange chromatography, reverse phase chromatography, andprecipitation from an appropriate solvent. Further processing of theproduct by for example ultrafiltration may also be employed.

A particularly preferred aspect of the present invention comprises amethod for the synthesis of an oligonucleotide comprising coupling anucleoside phosphoramidite, preferably a nucleoside 3′-phosphoramidite,with a nucleoside or nascent oligonucleotide comprising a free hydroxygroup, preferably a free 5′-hydroxy group, in the presence of anactivator, wherein the activator comprises a mixture of a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and anN-alkylimidazole, preferably N-methylimidazole.

In this particularly preferred embodiment, the phosphoramidite commonlycomprises a moiety of formula —P(OCH₂CH₂CN)N(CH(CH₃)₂)₂. Commonly, inthis embodiment, the concentration of each of the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and N-alkylimidazoleis from 0.1 to 0.25M, and preferably the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to N-alkylimidazoleis about 1:1 to about 1:1.5:1, most preferably 1:1. In this particularlypreferred embodiment, the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to phosphoramidite ispreferably from 0.5:1 to 2:1.

The present invention is illustrated without limitation by the followingExamples.

EXAMPLE 1 Preparation a Salt Complex of1,1-Dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and Pyridine

1,1-Dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one was suspended inacetonitrile, and 1.1 eq. of pyridine with respect to the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one was added dropwise tothe suspension. The solution turned clear at the end of the addition,and a salt complex of 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-oneand pyridine separated out of the solution as a fine crystallinematerial. The crystals were washed with either ether or hexane to removetraces of pyridine and acetonitrile. ¹H NMR (DMSO) chemical shifts inppm: 8.8 (2H, s), 8.2 (1H, q), 8.0 (1H, q) and 7.6-7.9 (6H, m).

EXAMPLE 2 Preparation a Salt Complex of1,1-Dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and 3-Picoline

A salt complex of 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and3-picoline was prepare in the same manner as described in Example 1. ¹HNMR (DMSO) chemical shifts in ppm: 8.8 (1H, s), 8.72 (1H, d), 8.27 (1H,d), 8.0 (2H, d), 7.77-7.93 (6H, m) and 2.45 (3H, s).

EXAMPLE 3 Preparation a Salt Complex of1,1-Dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and N-Methylimidazole

1,1-Dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one was suspended inacetonitrile, and 1.1 eq. of N-methylimidazole with respect to the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one was added dropwise tothe suspension. The reaction mixture was concentrated under reducedpressure to form the crystalline salt which was washed with either etheror hexane to remove traces of N-methylimidazole and acetonitrile. ¹H NMR(DMSO) chemical shifts in ppm: 13.9 (1H, s), 9.03 (1H, s), 7.59-7.75(6H, m) and 3.88 (3H, s),

EXAMPLE 4 Synthesis of deoxyribo-oligonucleotides Using a Salt Complexof 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and an OrganicBase

Synthesis of the oligonucleotide was carried out on DNA synthesizerOligo Pilot II (Amersham Pharmacia Biotech). The standardphosphoramidite chemistry protocol was followed for the synthesis withslight modifications. The concentration of phosphoramidite monomers was0.1 M in acetonitrile. The salt complex of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and pyridine,3-picoline or N-methylimidazole was used in place of tetrazole as theactivator during the condensation step. The concentration of the saltcomplex was 0.25 M in acetonitrile. The coupling time used for the chainelongation using the 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-onesalt complex were similar to coupling times used when tetrazole isactivator. After the condensation step, the phosphite triester linkagewas converted either to stable phosphate triester with iodine solutionor to stable phosphorothioate triester with Beaucage reagent or3-amino-1,2,4,-dithiazole-5-thione. At the end of the synthesis, solidsupports linked with fully protected oligonucleotide were treated with10% t-butylamine in concentrated ammonium hydroxide for 16-20 hr at 50°C. in order to release the oligonucleotide and to remove theβ-cyanoethyl protecting groups and the nucleobase protecting groups. Thecrude oligonucleotides were analyzed by ion exchange HPLC, capillaryelectrophoresis and MALDI-TOF mass spectrometry and were compared tooligonucleotides prepared using tetrazole as the activator. Table 1describes the conditions used to synthesize phosphorothioateoligonucleotide sequence 5′ TCT-CCC-AGC-GTG-CGC-CAT 3′ (SEQ ID NO 1),and Table 2 describes the results obtained from the various syntheses.The salt complex illustrated in Tables 1 and 2 is1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one andN-methylimidazole. TABLE 1 Synthesis Parameters for synthesis of SEQ IDNO 1. Molar Activa- Equiv. of Solid Scale of equiv. of tor vs.sulfurizing Support synthesis Activator Amidite Amidite agent CPG-beads746 μmole Tetrazole 2.0 equ. 4.3 3.2 CPG-beads 737 μmole salt-complex2.0 equ. 4.0 3.3 CPG-beads 737 μmole salt-complex 1.5 equ. 3.3 3.3 RigidPS 626 μmole salt-complex 2.0 equ. 4.0 3.8 Rigid PS 600 μmole Tetrazole2.0 equ. 4.3 4.0

TABLE 2 Analysis and results of SEQ ID NO 1. Solid mol equ. of Total ODFLP by FLP by Mol. supports Scale Activator amidite units CGE HPLC Wt.CPG 746 μmol Tetrazole 2.0 equ. 84504 74% 77% 5688 beads CPG 737 μmolCom Salt 2.0 equ. 82134 77% 79% 5687 beads CPG 737 μmol Com. Salt 1.5equ. 82320 77% 79% 5689 beads Rigid PS 626 μmol Com. Salt 2.0 equ. 8071276% 76% 5686 Rigid PS 600 μmol Tetrazole 2.0 equ. 75006 73% 71% 5687FLP = full length product,CGE = capillary gel electrophoresis,HPLC = Ion exchange HPLC

While this invention has been particularly shown and described withreferences to preferred embodiments thereof, it will be understood bythose skilled in the art that various changes in form and details may bemade therein without departing from the scope of the inventionencompassed by the appended claims.

1-64. (canceled)
 65. A method of synthesizing an oligonucleotide usingphosphoramidite chemistry comprising coupling a nucleoside or a nascentoligonucleotide having a free hydroxy or thiol group and a nucleosidephosphoramidite in the presence of a coupling agent, wherein thecoupling agent is a 1,1-dioxo-1,2-dihydro-1×6-benzo[d]isothiazol-3-onerepresented by the following structural formula:

wherein: p is 0 or an integer from 1 to 4; X⁷ is O or S; R for eachoccurrence is a substituent.
 66. The method of claim 1, wherein each Rindependently is halo, a substituted or unsubstituted aliphatic group,—NR¹¹R¹², —OR¹³, —OC(O)R¹³, —C(O)OR¹³, cyano, a substituted orunsubstituted aryl, a substituted or unsubstituted heterocyclyl, —CHO,—COR¹³, —NHCOR¹³, a substituted or unsubstituted aralkyl, or —SR¹³; ortwo adjacent R groups taken together with the carbon atoms to which theyare attached form a six membered saturated or unsaturated ring; wherein:R¹¹ and R¹² are each, independently, —H, a substituted or unsubstitutedaliphatic group, a substituted or unsubstituted aryl group, asubstituted or unsubstituted aralkyl group; or together with thenitrogen to which they are attached form a heterocyclyl group; and R¹³is a substituted or unsubstituted aliphatic group, a substituted orunsubstituted aryl group, or a substituted or unsubstituted aralkylgroup.
 67. The method of claim 1, wherein an organic base is presentwith the coupling agent during the coupling reaction.
 68. The method ofclaim 3, wherein the organic base is an amine.
 69. The method of claim4, wherein the amine is a tertiary amine.
 70. The method of claim 5,wherein the tertiary amine is selected from the group consisting of atrialkylamine, a substituted or unsubstituted N-alkylpyrrolidine, asubstituted or unsubstituted N-arylpyrrolidine, a substituted orunsubstituted N-alkylpyrrole, a substituted or unsubstitutedN-arylpyrrole, a substituted or unsubstituted N-alkylmorpholine, asubstituted or unsubstituted N-arylmorpholine, a substituted orunsubstituted N-alkylpiperidine, a substituted or unsubstitutedN-arylpiperidine, a substituted or unsubstituted N,N-dialkylpiperazine,a substituted or unsubstituted N,N-diarylpiperazine, a substituted orunsubstituted N-alkyl-N-arylpiperazine, substituted or unsubstitutedquinuclidine, and a substituted or unsubstituted1,8-diazabicyclo[5.4.0]undec-7ene.
 71. The method of claim 4, whereinthe amine is a substituted or unsubstituted azaheterocyclyl compound.72. The method of claim 7, wherein the azaheterocyclyl compound isselected from the group consisting of a substituted or unsubstitutedpyrimidine, a substituted or unsubstituted 1-alkylpyrazole, asubstituted or unsubstituted 1-arylpyrazole, a substituted orunsubstituted pyrazine, a substituted or unsubstituted N-alkylpurine, asubstituted or unsubstituted N-arylpurine, a substituted orunsubstituted N-alkylpyrrole, a substituted or unsubstitutedN-arylpyrrole, a substituted or unsubstituted pyridine, a substituted orunsubstituted N-alkylimidazole, a substituted or unsubstitutedN-arylimidazole, a substituted or unsubstituted quinoline, a substitutedor unsubstituted isoquinoline, a substituted or unsubstitutedquinoxaline, a substituted or unsubstituted quinazoline, a substitutedor unsubstituted N-alkylindole, a substituted or unsubstitutedN-arylindole, a substituted or unsubstituted N-alkylbenzimidazole, asubstituted or unsubstituted N-arylbenzimidazole, a substituted orunsubstituted triazine, a substituted or unsubstituted thiazole, asubstituted or unsubstituted 1-alkyl-7-azaindole, a substituted orunsubstituted 1-aryl-7-azaindole, a substituted or unsubstitutedpyrrolidine, a substituted or unsubstituted morpholine, a substituted orunsubstituted piperidine, and a substituted or unsubstituted piperazine.73. The method of claim 8, wherein the azaheterocyclyl compound ispyridine, 3-methylpyridine, or N-methylimidazole.
 74. The method ofclaim 1, wherein the nucleoside phosphoramidite is a monomer.
 75. Themethod of claim 1, wherein the nucleoside phosphoramidite is a dimer.76. The method of claim 10, wherein the phosphoramidite is a3′-phosphoramidite represented by one of the following structuralformula:

wherein: each X¹ is, independently, —O— or —S—; each X² is,independently, —O—, —S—, or —NR¹⁴—; each X³ is, independently, —O—, —S—,—CH₂—, or —(CH₂)₂—; R¹ is an alcohol protecting group or a thioprotecting group; R² is —H, a substituted or unsubstituted aliphaticgroup, —F, —OR⁶, —NR⁷R⁸, or —SR⁹; R³ is —OCH₂CH₂CN, —SCH₂CH₂CN, asubstituted or unsubstituted aliphatic group, —OR¹⁰, —SR¹⁰,—O—CH₂CH₂—Si(CH₃)₂C₆H₅, —O—CH₂CH₂—S(O)₂—CH₂CH₃, —O—CH₂CH₂—C₆H₄—NO₂,—S—CH₂CH₂—Si(CH₃)₂C₆H₅, —S—CH₂CH₂—S(O)₂—CH₂CH₃, or —S—CH₂CH₂—C₆H₄—NO₂.;R⁴ and R⁵ are each, independently, a substituted or unsubstitutedaliphatic group, a substituted or unsubstituted aryl group, asubstituted or unsubstituted aralkyl; or R⁴ and R⁵ taken together withthe nitrogen to which they are bound form a heterocyclyl group; and R⁶is —H, a substituted or unsubstituted aliphatic group, a substituted orunsubstituted aryl group, a substituted or unsubstituted aralkyl, anhydroxy protecting group or —(CH₂)_(q)—NR¹⁸R¹⁹; R⁷ and R⁸ are each,independently, H, a substituted or unsubstituted aliphatic group, or anamine protecting group; or R⁷ and R⁸ taken together with the nitrogen towhich they are attached are a heterocyclyl group; and R⁹ is H, asubstituted or unsubstituted aliphatic group, or an thio protectinggroup; R¹⁰ is for each occurrence is, independently, a substituted orunsubstituted aliphatic group, a substituted or unsubstituted aryl groupor a substituted or unsubstituted aralkyl group, R¹⁴ is —H, an alkylgroup, an aryl group or an aralkyl group; R¹⁸ and R¹⁹ are each,independently, —H, a substituted or unsubstituted aryl group, asubstituted or unsubstituted heteroaryl group, a substituted orunsubstituted aliphatic group, a substituted or unsubstituted aralkylgroup, a substituted or unsubstituted heteroaralkyl group or an amineprotecting group; or R¹⁸ and R¹⁹ taken together with the nitrogen towhich they are attached form a heterocyclyl group; and q is an integerfrom 1 to about 6; and each B is, independently, —H, a natural orunnatural nucleobase, a protected natural or unnatural nucleobase, aheterocycle, or a protected heterocycle.
 77. A method according to claim1, wherein X⁷ is O and p is
 0. 78. A method according to claim 1,wherein the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to nucleosidephosphoramidite is in the range of from about 0.2:1 to 5:1.
 79. A methodof condensing an N-mer oligonucleotide or a nucleoside represented bythe following structural formula:

wherein: each X¹ is, independently, —O— or —S—; each X² is,independently, —O—, —S—, or —NR¹⁴—; each X³ is, independently, —O—, —S—,—CH₂—, or —(CH₂)₂—; each X⁴ is, independently, O or S; X⁵ is —OH or —SH;each R² is, independently, —H, a substituted or unsubstituted aliphaticgroup, —F —OR⁶, —NR⁷R⁸, or —SR⁹; each R³ is, independently, —OCH₂CH₂CN,—SCH₂CH₂CN, a substituted or unsubstituted aliphatic group, —OR¹⁰,—SR¹⁰, —O—CH₂CH₂—Si(CH₃)₂C₆H₅, —O—CH₂CH₂—S(O)₂—CH₂CH₃,—O—CH₂CH₂—C₆H₄—NO₂, —S—CH₂CH₂—Si(CH₃)₂C₆H₅, —S—CH₂CH₂—S(O)₂—CH₂CH₃, or—S—CH₂CH₂—C₆H₄—NO₂.; each R⁶ is, independently, H, a substituted orunsubstituted aliphatic group, a substituted or unsubstituted arylgroup, a substituted or unsubstituted aralkyl, an hydroxy protectinggroup or —(CH₂)_(q)—NR¹⁸R¹⁹; R⁷ and R⁸ are each, independently, H, asubstituted or unsubstituted aliphatic group, or an amine protectinggroup; or R⁷ and R⁸ taken together with the nitrogen to which they areattached are a heterocyclyl group; and R⁹ is H, a substituted orunsubstituted aliphatic group, or a thio protecting group; R¹⁰ is foreach occurrence is, independently, a substituted or unsubstitutedaliphatic group, a substituted or unsubstituted aryl group or asubstituted or unsubstituted aralkyl group, each R¹⁴ is, independently,—H, an alkyl group, an aryl group or an aralkyl group; R¹⁶ is a hydroxyprotecting group, a thio protecting group, an amino protecting group,—(CH₂)_(q)—NR¹⁸R¹⁹, a solid support, or a cleavable linker attached to asolid support; R¹⁸ and R¹⁹ are each, independently, —H, a substituted orunsubstituted aryl group, a substituted or unsubstituted heteroarylgroup, a substituted or unsubstituted aliphatic group, a substituted orunsubstituted aralkyl group, a substituted or unsubstitutedheteroaralkyl group or an amine protecting group; or R¹⁸ and R¹⁹ takentogether with the nitrogen to which they are attached form aheterocyclyl group; and q is an integer from 1 to about 6; each B is,independently, —H, a natural or unnatural nucleobase, a protectednatural or unnatural nucleobase, a heterocycle, or a protectedheterocycle; and n is zero or a positive integer; with a nucleosidephosphoramidite represented by the following formula:

wherein R², R³, X¹, X², X³ and B are as previously defined: R¹ is analcohol protecting group or a thio protecting group; and R⁴ and R⁵ areeach, independently, a substituted or unsubstituted aliphatic group, asubstituted or unsubstituted aryl group, a substituted or unsubstitutedaralkyl; or R⁴ and R⁵ taken together with the nitrogen to which they arebound form a heterocyclyl group; comprising the step of contacting theoligonucleotide or nucleoside with the nucleoside phosphoramidite and a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one represented by thefollowing structural formula:

wherein: p is 0 or an integer from 1 to 4; X⁷ is O and S; R for eachoccurrence is a substituent; thereby forming an (n+1) oligonucleotidehaving a 5′-terminal trivalent phosphorous linkage represented by thefollowing structural formula:


80. The method of claim 15, wherein each R independently is halo, asubstituted or unsubstituted aliphatic group, —NR¹¹R¹², —OR¹³,—OC(O)R¹³, —C(O)OR¹³, cyano, a substituted or unsubstituted aryl, asubstituted or unsubstituted heterocyclyl, —CHO, —COR¹³, —NHCOR¹³, asubstituted or unsubstituted aralkyl, or —SR¹³; or two adjacent R groupstaken together with the carbon atoms to which they are attached form asix membered saturated or unsaturated ring; wherein: R¹¹ and R¹² areeach, independently, —H, a substituted or unsubstituted aliphatic group,a substituted or unsubstituted aryl group, a substituted orunsubstituted aralkyl group; or together with the nitrogen to which theyare attached form a heterocyclyl group; and R¹³ is a substituted orunsubstituted aliphatic group, a substituted or unsubstituted arylgroup, or a substituted or unsubstituted aralkyl group.
 81. The methodof claim 15, wherein an organic base is present when the oligonucleotideor nucleoside is contacted with the phosphoramidite and the1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one.
 82. The method ofclaim 17, wherein the concentration of the organic base and the1,1-dioxo-1,2-dihydro-1-benzo[d]isothiazol-3-one is about 0.01 M toabout 2 M.
 83. The method of claim 15, wherein the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to nucleosidephosphoramidite is in the range of from about 0.2:1 to 5:1.
 84. Themethod of claim 15, further comprising the steps of: a) contacting the(n+1) oligonucleotide having a 5′-terminal trivalent phosphorous linkagewith an oxidizing or sulfurizing agent, thereby forming anoligonucleotide having a pentavalent phosphorous backbone represented bythe following structural formula:

b) optionally capping X⁵ groups which did not react with thephosphoramidite by reacting the X⁵ groups with an acid chloride or ananhydride; c) deprotecting the (n+1) oligonucleotide having apentavalent phosphorous backbone by reacting it with a reagent to removeR¹; d) optionally repeating the coupling step, oxidation orsulfurization step, the capping step and deprotection step one or moretimes.
 85. The method of claim 20, wherein the oxidation orsulfurization step is the final step and the oligonucleotide isrepresented by the following structural formula:

wherein: m is an integer greater than n.
 86. The method of claim 20,wherein the deprotection step is the final step and the oligonucleotideprepare is represented by the following structural formula:

wherein:
 87. A method according to claim 20, wherein R¹⁶ is a cleavablelinker attached to a solid support.
 88. The method of claim 20, wherein:a) the oligonucleotide is oxidized after each coupling step and theoligonucleotide is a phosphodiester oligonucleotide; b) theoligonucleotide is sulfurized after each coupling step and theoligonucleotide prepared is a phosphorothioate oligonucleotide; or c)the oligonucleotide is oxidized after at least one coupling step andsulfurized after at least one coupling step and the oligonucleotideprepared is a chimeric oligonucleotide.
 89. A method according to claims20, wherein X⁷ is O and p is
 0. 90. A mehod according to either claim 21or 22, wherein the oligonucleotide is subsequently purified.
 91. Amethod for the synthesis of an oligonucleotide comprising coupling anucleoside phosphoramidite with a nucleoside or nascent oligonucleotidecomprising a free hydroxy group, in the presence of an activator,wherein the activator comprises a mixture of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and anN-alkylimidazole.
 92. A method according to claim 27, wherein thenucleoside phosphoramidite is a nucleoside 3′-phosphoramidite, and thenucleoside or nascent oligonucleotide comprises a free 5′-hydroxy group.93. A method according to claim 27, wherein the N-alkylimidazole isN-methylimidazole.
 94. A method according to claim 29, wherein thephosphoramidite comprises a moiety of formula —P(OCH₂CH₂CN)N(CH(CH₃)₂)₂.95. A method according to claim 27, wherein the concentration of each ofthe 1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one and theN-alkylimidazole is from 0.1 to 0.25M.
 96. A method according to claim27, wherein the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to N-alkylimidazoleis from about 1:1 to about 1:1.5:1.
 97. A method according to claim 27,wherein the mole ratio of1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one to phosphoramidite isfrom 0.5:1 to 2:1.
 98. A method for the synthesis of an oligonucleotidewhich comprises: a) coupling a 5′-protected nucleoside phosphoramiditewith a nucleoside or nascent oligonucleotide comprising a free hydroxygroup and attached to a solid support by a clevable linker, in thepresence of a tertiary amine salt of1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one, thereby forming aphosphite triester; b) oxidizing or sulphurising the phosphite triesterto produce a 5′-protected phosphate or phosphorothioate triester; c)optionally capping unreacted hydroxy groups by reaction with a cappingagent; d) removing the 5′-protecting group from the 5′-protectedphosphate or phosphorothioate triester, to form a 5′-hydroxy group; e)repeating steps a) to d) one or more times until a desiredoligonucleotide sequence is assembled; f) deprotecting theoligonucleotide, cleaving the oligonucleotide from the solid support,and purifying the oligonucleotide.
 99. A salt complex comprising anN-alkylimidazole and a1,1-dioxo-1,2-dihydro-1λ⁶-benzo[d]isothiazol-3-one represented by thefollowing structural formula:

wherein: p is 0 or an integer from 1 to 4; X⁷ is O or S; and R for eachoccurrence is a substituent.
 100. A salt complex according to claim 35,wherein p is 0, X⁷ is O and the N-alkylimidazole is N-methylimidazole.